An analytical approach is developed for reconstructing site-specific methyl-bearing protein side-chain conformational energy surfaces from NMR methyl axis order parameters (O(axis)(2)). Application of an enhanced sampling algorithm (adaptive biasing force) to molecular dynamics simulation of a protein, calcium-bound calmodulin, reveals a nonlinear correlation between O(axis)(2) and the populations of rotamer states of protein side-chains, permitting the rotamer populations to be extracted directly from O(axis)(2). The analytical approach yields side-chain conformational distributions that are in excellent agreement with those obtained from the enhanced-sampling MD results.
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http://dx.doi.org/10.1021/jp2104853 | DOI Listing |
Int J Mol Sci
January 2025
Faculty of Chemistry and Pharmacy, University of Opole, Oleska 48, 45-052 Opole, Poland.
O-Methyldehydroserine, ΔSer(Me), is a non-standard α,β-dehydroamino acid, which occurs naturally in Cyrmenins with potential pharmaceutical application. The C-terminal part and the side chain of the ΔSer(Me) residue constitute the β-methoxyacrylate unit, responsible for antifungal activity of Cyrmenins. The short model, Ac-ΔSer(Me)-OMe, was analyzed considering the geometrical isomer Z () and E ().
View Article and Find Full Text PDFBioinformatics
January 2025
Department of Molecular Genetics, University of Toronto, Ontario, M5S 3K3, Canada.
Motivation: Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design.
Results: Here we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime.
Int J Mol Sci
December 2024
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
Living systems cannot rely on random intermolecular approaches toward cell crowding, and hidden mechanisms must be present to favor only those molecular interactions required explicitly by the biological function. Electromagnetic messaging among proteins is proposed from the observation that charged amino acids located on the protein surface are mostly in adjacent sequence positions and/or in spatial proximity. Molecular dynamics (MD) simulations have been used to predict electric charge proximities arising from concerted motions of charged amino acid side chains in two protein model systems, human ubiquitin and the chitinolytic enzyme from .
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
January 2025
Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
Acc Chem Res
January 2025
Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States.
ConspectusProtein higher-order structure (HOS) is key to biological function because the mechanisms of protein machinery are encoded in protein three-dimensional structures. Mass spectrometry (MS)-based protein footprinting is advancing protein structure characterization by mapping solvent-accessible regions of proteins and changes in H-bonding, thereby providing higher order structural information. Footprinting provides insights into protein dynamics, conformational changes, and interactions, and when conducted in a differential way, can readily reveal those regions that undergo conformational change in response to perturbations such as ligand binding, mutation, thermal stress, or aggregation.
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